Abstract 1460: Decoding the tumor biology of the orphan malignancy fibrolamellar carcinoma at single-cell resolution
Authors: Alaa R. Farghli, Bo Shui, Seoyeon Lee, Paul R. Munn, Yutong Zhu, Paul Soloway, Praveen Sethupathy
Journal: Cancer Research (2022)

Abstract The World Health Organization (WHO) recognized fibrolamellar carcinoma (FLC) in 2010 as a rare and aggressive form of liver cancer that predominately afflicts adolescents and young adults. There are currently no effective therapies. Surgical resection remains the only option to date, but it is not viable for patients who present with metastasis. Thus, there is an urgent need to identify therapeutic targets. The hallmark genetic lesion of FLC, occurring in &amp;gt;80% of patients, was recently identified to be a ~400kb heterozygous deletion on chromosome 19, leading to the oncogenic fusion protein DNAJB1-PRKACA (DP). We recently used FLC primary tumors and matched non-malignant liver samples to map the chromatin activity landscape of FLC by chromatin run-on sequencing, or ChRO-seq, which is a state-of-the-art technology for quantifying nascent transcription and defining active regulatory elements across the genome. We identified nearly 7000 FLC-specific enhancers and ~150 “super-enhancers” (SEs) - dense clusters of highly active enhancers that mark nearby critical oncogenes. Despite these advances, a major limitation is the bulk tissue nature of the study - that is, these data reflect an average profile across numerous different cell types (hepatocytes, stellate cells, fibroblasts, macrophages, endothelial cells, etc.), and therefore it is not evident which enhancers and genes are active in which cell types. This represents a major knowledge gap. If we could learn the specific cell types in which FLC enhancers and genes are active, we could then study the functions of these genes in FLC with greater precision and develop more effective targeted therapeutics. I recently conducted single-cell Assay for Transposase Accessible Chromatin ATAC-seq (scATAC-seq) to bridge this knowledge gap. I identified eight clusters from FLC-Primary, FLC-Metastatic, and non-malignant liver (NML) samples. Dimensionality reduction reveals two FLC-Primary, and FLC-Metastatic derived clusters that exhibit an epithelial-like identity most closely related to NML-epithelial cells. Using this scATAC-seq dataset, I have deconvoluted and resolved the bulk resolution limitations of ChRO-seq signal. ScATAC-seq reveals ChRO-seq defined candidate genes are highly accessible in FLC-Primary and FLC-Metastatic transformed Epithelial Cells. I have also dissected ChRO-seq defined SE’s and detailed the proportion of active constituent enhancers within each cell type. Further analysis revealed cell-type-specific transcriptional networks. Together, these studies provide the first single-cell resolution understanding of the transcriptional network in FLC. Citation Format: Alaa R. Farghli, Bo Shui, Seoyeon Lee, Paul R. Munn, Yutong Zhu, Paul Soloway, Praveen Sethupathy. Decoding the tumor biology of the orphan malignancy fibrolamellar carcinoma at single-cell resolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1460.